Rice (Oryza sativa L.), one of the major food crop and staple food for more than half of the population around the globe. Compare to japonica rice, indica rice has been less responsive to invitro culture. Moreover considerable variations in regeneration efficiency among a multiplicity of rice cultivars, especially between japonica and indica rice varieties also exist. Therefore, a comprehensive understanding of somatic embryogenesis and regeneration events may provide a better understanding of the order-generating process. In the present study, a genome wide time course array was conducted to monitor the differences in gene expression pattern during somatic embryogenesis and regeneration process between japonica and indica rice subspecies. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between japonica and indica rice cultivars at six different developmental stages of somatic embryogenesis and regeneration in rice. Callus induction was carried out using 2, 4 -D followed by TDZ (Cytokinin) mediated somatic embryo induction and further differentiation. Global gene expression among different samples showed greater complexity in japonica rice compare to indica.